gen_mixture

snap_simulate.system.gen_mixture(params, outfile=None)

This function generates an initial system snapshot frame, placing molecules/particles without overlaps, and writes the snapshot to a GSD file.

Parameters

• params (dict): A system configuration dictionary containing the setup parameters. The configuration sections (described below) must all be top-level keys in this dictionary.

• outfile (str): The output GSD file path (e.g. "system.gsd") where the generated snapshot frame will be written.

Configuration Sections

The following keys should be defined inside the params dictionary:

• particles (required): Physical specifications for each particle type. (See particles).

• molecules (required): Definition of molecule structures and count specifications. (See molecules).

• box (required): Cell boundaries and placement settings. (See box).

• bonds (optional): Bond types and specifications.

• angles (optional): Angle types and specifications.

• dihedrals (optional): Dihedral types and specifications.

Builder Components

The component-specific system builders and parameters are documented in detail below:

• particles
• molecules
• box